Table 3.
“Module-based” methods.
| Method | Module Definition | # of Conditions | Citation | Availability |
| DICER | Unbiased | Multiple | [63] | Bioconductor R package (dcanr) Java software at http://acgt.cs.tau.ac.il/dicer/ |
| DiffCoEx | Unbiased | Multiple | [64] | R package at https://github.com/ddeweerd/MODifieRDev.git Bioconductor R package (dcanr) |
| M-Modules | Unbiased | Multiple | [65] | |
| NIPD | Unbiased | Multiple | [66] | |
| C3D | Unbiased | Multiple | [67] | |
| CoXpress | Unbiased | Two | [68] | R package at http://coxpress.sourceforge.net/ |
| DiffCorr | Unbiased | Two | [69] | CRAN R package (DiffCorr) |
| ModMap | Unbiased | Two | [70] | Java executable at http://acgt.cs.tau.ac.il/modmap/ |
| ALPACA | Unbiased | Two | [71] | R package at https://github.com/meghapadi/ALPACA |
| BFDCA | Unbiased | Two | [59] | R package at http://dx.doi.org/10.17632/jdz4vtvnm3.1 |
| DiffCoMO | Unbiased | Two | [72] | |
| SCDA | Unbiased | Two | [73] | MATLAB implementation at http://vk.cs.umn.edu/SDC/ |
| CODC | Unbiased | Two | [60] | R package at https://github.com/Snehalikalall/CODC |
| EgoNet | Unbiased | Two | [74] | |
| BicMix | Unbiased | Two | [75] | R package at https://github.com/chuangao/BicMix |
| MODA | Unbiased | Two | [76] | Bioconductor R package (MODA) |
| COSINE | Unbiased | Two | [77] | CRAN R package (COSINE) |
| DECluster | Unbiased | Two | [78] | |
| DEDC | Unbiased | Two | [79] | |
| DCN | Unbiased | Two | [57] | R package at https://github.com/weiliu123/DCN-package |
| Contrast Subgraph | Unbiased | Two | [80] | |
| DCIM | Unbiased | De novo | [81] | |
| GSCA | A priori | Two | [82] | Bioconductor R package (GSCA) |
| ScorePAGE | A priori | Two | [83] | |
| IB-GSA | A priori | Two | [84] | |
| Gill | A priori | Two | [48] | R package at http://www.somnathdatta.org/Supp/DNA |
| CoGa | A priori | Two | [85] | |
| dCoxS | A priori pairs of gene sets | Two | [86] | R function at http://www.snubi.org/publication/dCoxS/ |
| MAGIC | A priori pairs of gene sets | Two | [44] | Bioconductor R package (dcanr) MATLAB implementation at https://github.com/chiuyc/MAGIC |
| ESEA | Structured pathway | Two | [87] | R package on CRAN (ESEA) |
| PWEA | Structured pathway | Two | [88] | R package on Bioconductor (ToPASeq) |
| KEDDY | Structured pathway | Two | [89] | Java implementation at https://sites.google.com/site/sjunggsm/keddy |
| kDDN | Structured pathway | Two | [90] | MATLAB implementation at http://www.cbil.ece.vt.edu/software.htm |